Contacts of the strand formed by residues 122 - 128 (chain C) in PDB entry 2OB1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 122 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C LEU* 3.7 39.0 - - + -
97C GLU 4.5 0.8 + - - +
99C VAL* 3.4 8.5 - - + +
101C VAL* 3.8 22.7 - - + -
115C LEU* 4.2 27.6 - - + -
116C LEU* 3.5 18.3 - - + +
119C PHE* 3.0 23.2 + - + +
120C PRO 3.4 0.2 - - - -
121C HIS* 1.3 79.4 - - - +
123C ALA* 1.3 69.2 + - - +
124C TYR* 4.2 11.2 - - + -
168C ARG* 2.9 29.5 + - - +
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C VAL 2.9 10.7 + - - +
100C GLN* 3.2 11.7 - - + -
101C VAL* 2.6 33.5 + - - +
121C HIS 3.9 0.8 + - - +
122C LEU* 1.3 78.1 - - - +
124C TYR* 1.3 56.8 + - - +
125C VAL* 5.4 2.9 - - + -
168C ARG* 3.3 20.2 - - + +
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Residues in contact with TYR 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 3.4 31.4 - - + -
103C ASN* 2.7 38.4 + - + +
109C ASP* 4.5 1.0 - - - +
111C ARG* 3.5 16.2 + - + +
112C MET* 3.5 45.8 + - + -
115C LEU* 4.0 12.1 - - + -
116C LEU* 4.2 3.6 - - + -
122C LEU* 4.2 13.2 - - + -
123C ALA* 1.3 75.3 - - - +
125C VAL* 1.3 79.7 - - - +
126C ASP* 3.2 23.6 - - - -
168C ARG 2.7 14.1 + - - +
169C TYR* 3.3 12.7 - + + -
170C LYS* 2.9 25.5 + - - +
199C ILE* 4.3 1.1 - - + +
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLN* 5.7 3.1 - - + -
101C VAL 2.6 14.5 + - - +
102C VAL* 4.4 7.6 - - + +
103C ASN* 2.8 32.2 + - - +
123C ALA* 5.4 3.1 - - + -
124C TYR* 1.3 82.8 - - - +
126C ASP* 1.3 60.0 + - - +
127C ILE* 3.8 25.1 + - + -
162C PHE* 5.5 1.6 - - + -
170C LYS* 3.5 16.6 - - + +
172C ALA* 5.5 1.3 - - + -
189C CYS* 3.6 50.9 - - + +
190C THR* 4.4 7.4 - - + -
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ASN* 3.5 5.2 + - - +
106C CYS* 2.9 28.5 - - - +
109C ASP 4.9 0.7 - - - +
112C MET* 4.0 3.1 - - - +
124C TYR* 3.2 19.5 - - - -
125C VAL* 1.3 73.0 - - - +
127C ILE* 1.3 63.4 + - - +
136C LYS* 2.9 18.7 + - - -
169C TYR* 2.5 37.0 + - + +
170C LYS 2.8 13.3 + - - +
171C LEU* 3.4 10.2 - - + +
172C ALA* 3.0 25.8 + - - +
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C VAL* 3.9 26.0 - - + -
103C ASN 2.9 12.4 + - - +
104C LEU* 4.2 11.4 - - + -
105C GLY 2.7 31.2 + - - -
106C CYS* 3.0 8.9 + - - -
125C VAL* 3.8 17.9 - - + -
126C ASP* 1.3 79.3 - - - +
128C ASP* 1.3 63.0 + - - +
172C ALA* 3.4 8.3 - - + +
174C CYS* 3.3 32.5 - - + -
176C LEU* 4.0 16.2 - - + -
182C THR* 5.7 2.5 - - + -
185C LEU* 4.5 14.8 - - + -
186C LEU* 4.2 15.5 - - + -
189C CYS* 5.4 0.7 - - - -
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Residues in contact with ASP 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C GLY* 3.5 20.8 - - - -
106C CYS* 3.9 6.5 - - - -
107C GLY* 2.8 24.6 + - - -
127C ILE* 1.3 76.6 - - - +
129C TYR* 1.3 88.5 + - - +
132C SER* 2.9 23.0 + - - +
133C VAL* 3.4 16.6 - - + +
172C ALA 3.3 3.6 + - - -
173C ALA* 3.3 5.5 - - - -
174C CYS 2.9 25.8 + - - -
176C LEU* 5.6 3.7 - - - +
203C LEU* 5.5 0.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il